Transcriptome analysis based on high-throughput sequencing of a cDNA library has been widely applied to functional genomic studies.However,the cDNA dependence of most RNA sequencing techniques constrains their ability...Transcriptome analysis based on high-throughput sequencing of a cDNA library has been widely applied to functional genomic studies.However,the cDNA dependence of most RNA sequencing techniques constrains their ability to detect base modifications on RNA,which is an important element for the post-transcriptional regulation of gene expression.To comprehensively profile the N^(6)-methyladenosine(m^(6)A)and N^(5)-methylcytosine(m5 C)modifications on RNA,direct RNA sequencing(DRS)using the latest Oxford Nanopore Technology was applied to analyze the transcriptome of six tissues in rice.Approximately 94 million reads were generated,with an average length ranging from 619 nt to 1013 nt,and a total of 45,707 transcripts across 34,763 genes were detected.Expression profiles of transcripts at the isoform level were quantified among tissues.Transcriptome-wide mapping of m^(6)A and m5 C demonstrated that both modifications exhibited tissue-specific characteristics.The transcripts with m^(6)A modifications tended to be modified by m5 C,and the transcripts with modifications presented higher expression levels along with shorter poly(A)tails than transcripts without modifications,suggesting the complexity of gene expression regulation.Gene Ontology analysis demonstrated that m^(6)A-and m5 C-modified transcripts were involved in central metabolic pathways related to the life cycle,with modifications on the target genes selected in a tissue-specific manner.Furthermore,most modified sites were located within quantitative trait loci that control important agronomic traits,highlighting the value of cloning functional loci.The results provide new insights into the expression regulation complexity and data resource of the transcriptome and epitranscriptome,improving our understanding of the rice genome.展开更多
Reconfigurable intelligent surface(RIS)-assisted symbiotic radio is a spectrum-and energy-efficient communication paradigm,in which an RIS performs passive beamforming to enhance active transmission,while using the el...Reconfigurable intelligent surface(RIS)-assisted symbiotic radio is a spectrum-and energy-efficient communication paradigm,in which an RIS performs passive beamforming to enhance active transmission,while using the electromagnetic waves from the active transmission for additional information transfer(i.e.,passive transmission).In this paper,a hybrid RIS-based modulation,termed hybrid phase and code modulation(HPCM),is proposed to improve the reliability of RIS-assisted symbiotic radio.In RIS-HPCM,the RIS simultaneously performs direct sequence spread spectrum and passive beamforming on incident signals.Moreover,both the spreading code and phase offset are exploited to carry the RIS’s own information.A low-complexity detector is designed,in which the receiver first detects the spreading codes and then demodulates the constellation symbols.We analyze the bit error rate(BER)performance of RIS-HPCM over Rician fading channels.BER upper bounds and approximate BER expressions are derived in closed-form for maximum-likelihood and low-complexity detectors,respectively.Simulation results in terms of BER verify the analysis and show the superiority of RIS-HPCM over the existing RIS-based modulation.展开更多
Geminiviruses, in particular the members of the genus Begomovirus , are considered to be a major phytosanitary problem for tomato crops production in the world. They are responsible for yield losses of up to 20% to 10...Geminiviruses, in particular the members of the genus Begomovirus , are considered to be a major phytosanitary problem for tomato crops production in the world. They are responsible for yield losses of up to 20% to 100%. Regrettably, Togo is not spared from this situation. This work aims to show the genetic diversity of the begomoviruses affecting tomato crops production in Togo and their relationship with other begomoviruses. To achieve these objectives, 307 samples of tomato leaves and wild plant species with typical virus symptoms were collected in the Maritime, Plateaus, Central, Kara and Savannah regions and submitted to PCR analysis. The results revealed the presence of begomovirus in 25.40% of the analyzed samples. The PCR products obtained were submitted to direct sequencing. Phylogenetic analysis of sequences of DNA-A different regions of begomovirus identified in this work with that of other begomoviruses showed a nucleotide identity of 96% respectively for Tomato leaf curl Togo virus-Fontem, Tomato Leaf Curl Togo Virus , Ageratum leaf curl Cameroon Alphasatellite;98% respectively to Tomato leaf curl Nigeria virus , Ageratum leaf curl Cameroon virus , Tomato leaf curl Cameroon virus-Fontem, Ageratum leaf curl Cameroon virus and 99% respectively to Tomato leaf curl Kumasi virus , Pepper yellow vein Mali virus Bazegahot and Pepper yellow vein Mali virus-Ouaga. These results suggest a high degree of genetic diversity of tomato begomoviruses identified in Togo.展开更多
A novel algorithm is proposed to resolve the defects in the traditional linear frequency modulation(LFM)jamming suppression algorithm in the fractional Fourier transform(FRFT)domain.The traditional LFM jamming suppres...A novel algorithm is proposed to resolve the defects in the traditional linear frequency modulation(LFM)jamming suppression algorithm in the fractional Fourier transform(FRFT)domain.The traditional LFM jamming suppression algorithm in the FRFT domain has some defects.For example,the exact threshold is difficult to set and both the signal-to-noise ratio(SNR)loss and spectrum leakage are serious in strong jamming-to-signal ratio(JSR)situations.Windowing,overlapping and inverse windowing techniques are used in the FRFT domain to reduce the spectrum leakage and the SNR loss.Under the condition that only the direct sequence spread spectrum(DSSS)signal and white Gaussian noise are present,the amplitude of the received signal after FRFT is assumed to be Rayleigh distributed.Based on the distribution characteristic,hypothesis testing is used to suppress the jamming spectrum using the algorithm.Simulation results show that the performance of proposed algorithm is better than that of the conventional algorithms,especially in a strong jamming and multi component LFM jamming environment.展开更多
Tomato fruit are sensitive to chilling injury(CI)during cold storage.Several factors have been discovered to be involved in chilling injury of tomato fruit.Plant hormones play an important regulatory role,however,the ...Tomato fruit are sensitive to chilling injury(CI)during cold storage.Several factors have been discovered to be involved in chilling injury of tomato fruit.Plant hormones play an important regulatory role,however,the relationship between chilling injury and N6-methyladenosine(m^(6)A)methylation of transcripts in plant hormone pathways has not been reported yet.In order to clarify the complex regulatory mechanism of m^(6)A methylation on chilling injury in tomato fruit,Nanopore direct RNA sequencing was employed.A large number of enzymes and transcription factors were found to be involved in the regulation process of fruit chilling injury,which were associated with plant hormone,such as 1-aminocyclopropane 1-carboxylate synthase(ACS),aspartate aminotransferase(AST),auxin response factor(ARF2),ethylene response factor 2(ERF2),gibberellin 20-oxidase-3(GA20ox)and jasmonic acid(JA).By conjoint analysis of the differential expression transcripts related to chilling injury andm^(6)Amethylation differential expression transcripts 41 differential expression transcripts were identified involved in chilling injury including 1-aminocyclopropane-1-carboxylate oxidase(ACO)and pectinesterase(PE)were down-regulated and heat shock cognate 70 kD protein 2(cpHSC70),HSP70-binding protein(HspBP)and salicylic acid-binding protein 2(SABP2)were up-regulated.Our results will provide a deeper understanding for chilling injury regulatory mechanism and post-harvest cold storage of tomato fruit.展开更多
With the goal of achieving high stability and reliability to support underwater point-to-point communications and code division multiple access(CDMA) based underwater networks, a direct sequence spread spectrum based ...With the goal of achieving high stability and reliability to support underwater point-to-point communications and code division multiple access(CDMA) based underwater networks, a direct sequence spread spectrum based underwater acoustic communication system using dual spread spectrum code is proposed. To solve the contradictions between the information data rate and the accuracy of Doppler estimation, channel estimation, and frame synchronization, a data frame structure based on dual spread spectrum code is designed. A long spread spectrum code is used as the training sequence, which can be used for data frame detection and synchronization, Doppler estimation, and channel estimation. A short spread spectrum code is used to modulate the effective information data. A delay cross-correlation algorithm is used for Doppler estimation, and a correlation algorithm is used for channel estimation. For underwater networking, each user is assigned a different pair of spread spectrum codes. Simulation results show that the system has a good anti-multipath, anti-interference, and anti-Doppler performance, the bit error rate can be smaller than 10^(-6) when the signal-to-noise ratio is larger than-10 dB, the data rate can be as high as 355 bits/s, and the system can be used in the downlink of CDMA based networks.展开更多
The Human Genome Project opened an era of(epi)genomic research,and also provided a platform for the development of new sequencing technologies.During and after the project,several sequencing technologies continue to d...The Human Genome Project opened an era of(epi)genomic research,and also provided a platform for the development of new sequencing technologies.During and after the project,several sequencing technologies continue to dominate nucleic acid sequencing markets.Currently,Illumina(short-read),PacBio(long-read),and Oxford Nanopore(longread)are the most popular sequencing technologies.Unlike PacBio or the popular short-read sequencers before it,which,as examples of the second or so-called Next-Generation Sequencing platforms,need to synthesize when sequencing,nanopore technology directly sequences native DNA and RNA molecules.Nanopore sequencing,therefore,avoids converting mRNA into cDNA molecules,which not only allows for the sequencing of extremely long native DNA and full-length RNA molecules but also document modifications that have been made to those native DNA or RNA bases.In this review on direct DNA sequencing and direct RNA sequencing using Oxford Nanopore technology,we focus on their development and application achievements,discussing their challenges and future perspective.We also address the problems researchers may encounter applying these approaches in their research topics,and how to resolve them.展开更多
Based on the brief account of the performance analysis result of the direct sequence spread spectrum(DSSS)system against a single tone continuous wave(CW)interference obtained from the traditional standard Gaussian ap...Based on the brief account of the performance analysis result of the direct sequence spread spectrum(DSSS)system against a single tone continuous wave(CW)interference obtained from the traditional standard Gaussian approximation(SGA)hypothesis,the mathematical expression of the interference component of the symbol decision variable in the periodic sequence DSSS system under CW interference was deduced and the actual performance of the periodic sequence DSSS system against CW interference was researched through theoretical analysis and numerical simulations.The results indicate that the interference component of the symbol decision variable in the periodic sequence DSSS system under CW interference operates at a constant level or fluctuate monochromatically,which does not approach the standard Gaussian distribution,and the actual performance of the periodic sequence DSSS system against CW interference is completely different from the analytic result resorted to the standard Gaussian approximation(SGA).The bit error performance is correlative not only with the interference-signal ratio(ISR),the frequency offset and the phase of the CW interference sensitively,but also with the individual spread spectrum code sequence.展开更多
Direction of arrival(DOA)estimation is one of the key technologies in smart antennas in the direct sequence ultra wideband(DS-UWB)system.Traditional DOA estimation methods based on narrow-band signals are not suitable...Direction of arrival(DOA)estimation is one of the key technologies in smart antennas in the direct sequence ultra wideband(DS-UWB)system.Traditional DOA estimation methods based on narrow-band signals are not suitable for such system.Therefore,a fourth-order cumulant-based estimation method of DOA for DS-UWB signal is proposed.This method is set on the frequency domain model of DS-UWB array signal.Simulation results show that the algorithm is effective and can guarantee adequate estimation accuracy.展开更多
基金supported by the National Natural Science Foundation of China(Grant No.31671775).
文摘Transcriptome analysis based on high-throughput sequencing of a cDNA library has been widely applied to functional genomic studies.However,the cDNA dependence of most RNA sequencing techniques constrains their ability to detect base modifications on RNA,which is an important element for the post-transcriptional regulation of gene expression.To comprehensively profile the N^(6)-methyladenosine(m^(6)A)and N^(5)-methylcytosine(m5 C)modifications on RNA,direct RNA sequencing(DRS)using the latest Oxford Nanopore Technology was applied to analyze the transcriptome of six tissues in rice.Approximately 94 million reads were generated,with an average length ranging from 619 nt to 1013 nt,and a total of 45,707 transcripts across 34,763 genes were detected.Expression profiles of transcripts at the isoform level were quantified among tissues.Transcriptome-wide mapping of m^(6)A and m5 C demonstrated that both modifications exhibited tissue-specific characteristics.The transcripts with m^(6)A modifications tended to be modified by m5 C,and the transcripts with modifications presented higher expression levels along with shorter poly(A)tails than transcripts without modifications,suggesting the complexity of gene expression regulation.Gene Ontology analysis demonstrated that m^(6)A-and m5 C-modified transcripts were involved in central metabolic pathways related to the life cycle,with modifications on the target genes selected in a tissue-specific manner.Furthermore,most modified sites were located within quantitative trait loci that control important agronomic traits,highlighting the value of cloning functional loci.The results provide new insights into the expression regulation complexity and data resource of the transcriptome and epitranscriptome,improving our understanding of the rice genome.
基金supported in part by the National Natural Science Foundation of China under Grant 62201228 and Grant 62001190in part by the Science and Technology Major Project of Tibetan Autonomous Region of China under Grant No.XZ202201ZD0006G02.
文摘Reconfigurable intelligent surface(RIS)-assisted symbiotic radio is a spectrum-and energy-efficient communication paradigm,in which an RIS performs passive beamforming to enhance active transmission,while using the electromagnetic waves from the active transmission for additional information transfer(i.e.,passive transmission).In this paper,a hybrid RIS-based modulation,termed hybrid phase and code modulation(HPCM),is proposed to improve the reliability of RIS-assisted symbiotic radio.In RIS-HPCM,the RIS simultaneously performs direct sequence spread spectrum and passive beamforming on incident signals.Moreover,both the spreading code and phase offset are exploited to carry the RIS’s own information.A low-complexity detector is designed,in which the receiver first detects the spreading codes and then demodulates the constellation symbols.We analyze the bit error rate(BER)performance of RIS-HPCM over Rician fading channels.BER upper bounds and approximate BER expressions are derived in closed-form for maximum-likelihood and low-complexity detectors,respectively.Simulation results in terms of BER verify the analysis and show the superiority of RIS-HPCM over the existing RIS-based modulation.
基金the West African Agricultural Productivity Program(WAAPP/TOGO)and Bill and Melinda Gates Foundation(BMGF)for supporting this project.
文摘Geminiviruses, in particular the members of the genus Begomovirus , are considered to be a major phytosanitary problem for tomato crops production in the world. They are responsible for yield losses of up to 20% to 100%. Regrettably, Togo is not spared from this situation. This work aims to show the genetic diversity of the begomoviruses affecting tomato crops production in Togo and their relationship with other begomoviruses. To achieve these objectives, 307 samples of tomato leaves and wild plant species with typical virus symptoms were collected in the Maritime, Plateaus, Central, Kara and Savannah regions and submitted to PCR analysis. The results revealed the presence of begomovirus in 25.40% of the analyzed samples. The PCR products obtained were submitted to direct sequencing. Phylogenetic analysis of sequences of DNA-A different regions of begomovirus identified in this work with that of other begomoviruses showed a nucleotide identity of 96% respectively for Tomato leaf curl Togo virus-Fontem, Tomato Leaf Curl Togo Virus , Ageratum leaf curl Cameroon Alphasatellite;98% respectively to Tomato leaf curl Nigeria virus , Ageratum leaf curl Cameroon virus , Tomato leaf curl Cameroon virus-Fontem, Ageratum leaf curl Cameroon virus and 99% respectively to Tomato leaf curl Kumasi virus , Pepper yellow vein Mali virus Bazegahot and Pepper yellow vein Mali virus-Ouaga. These results suggest a high degree of genetic diversity of tomato begomoviruses identified in Togo.
基金National Natural Science Foundation of China(61175059)the Natural Science Foundation of Hebei Province(F2011205023)。
文摘A novel algorithm is proposed to resolve the defects in the traditional linear frequency modulation(LFM)jamming suppression algorithm in the fractional Fourier transform(FRFT)domain.The traditional LFM jamming suppression algorithm in the FRFT domain has some defects.For example,the exact threshold is difficult to set and both the signal-to-noise ratio(SNR)loss and spectrum leakage are serious in strong jamming-to-signal ratio(JSR)situations.Windowing,overlapping and inverse windowing techniques are used in the FRFT domain to reduce the spectrum leakage and the SNR loss.Under the condition that only the direct sequence spread spectrum(DSSS)signal and white Gaussian noise are present,the amplitude of the received signal after FRFT is assumed to be Rayleigh distributed.Based on the distribution characteristic,hypothesis testing is used to suppress the jamming spectrum using the algorithm.Simulation results show that the performance of proposed algorithm is better than that of the conventional algorithms,especially in a strong jamming and multi component LFM jamming environment.
基金supported by grants from the National Natural Science Foundation of China(Grant Nos.31772022,32072284 and 31501544)the Special Innovation Ability Construction Fund of Beijing Academy of Agricultural and Forestry Sciences(Grant Nos.20200427 and 20210437)+4 种基金Science and Technology Planning Project of Tianjin City(Grant No.19YFSLQY00100)the Beijing Municipal Science and Technology Commission(Grant Nos.Z191100008619004 and Z191100004019010)Supported by China Agriculture Research System of MOF and MARA,collaborative innovation center of Beijing Academy of Agricultural and Forestry Sciences(Grant No.201915)the Young Investigator Fund of Beijing Academy of Agricultural and Forestry Sciences(Grant No.202016)the key scientific research projects of colleges and universities in Henan Province(Grant No.20A550014)。
文摘Tomato fruit are sensitive to chilling injury(CI)during cold storage.Several factors have been discovered to be involved in chilling injury of tomato fruit.Plant hormones play an important regulatory role,however,the relationship between chilling injury and N6-methyladenosine(m^(6)A)methylation of transcripts in plant hormone pathways has not been reported yet.In order to clarify the complex regulatory mechanism of m^(6)A methylation on chilling injury in tomato fruit,Nanopore direct RNA sequencing was employed.A large number of enzymes and transcription factors were found to be involved in the regulation process of fruit chilling injury,which were associated with plant hormone,such as 1-aminocyclopropane 1-carboxylate synthase(ACS),aspartate aminotransferase(AST),auxin response factor(ARF2),ethylene response factor 2(ERF2),gibberellin 20-oxidase-3(GA20ox)and jasmonic acid(JA).By conjoint analysis of the differential expression transcripts related to chilling injury andm^(6)Amethylation differential expression transcripts 41 differential expression transcripts were identified involved in chilling injury including 1-aminocyclopropane-1-carboxylate oxidase(ACO)and pectinesterase(PE)were down-regulated and heat shock cognate 70 kD protein 2(cpHSC70),HSP70-binding protein(HspBP)and salicylic acid-binding protein 2(SABP2)were up-regulated.Our results will provide a deeper understanding for chilling injury regulatory mechanism and post-harvest cold storage of tomato fruit.
基金Project supported by the National Natural Science Foundation of China(Nos.61431005,51409235,and 61401111)the Fundamental Research Funds for the Central Universities,China(No.201213004)
文摘With the goal of achieving high stability and reliability to support underwater point-to-point communications and code division multiple access(CDMA) based underwater networks, a direct sequence spread spectrum based underwater acoustic communication system using dual spread spectrum code is proposed. To solve the contradictions between the information data rate and the accuracy of Doppler estimation, channel estimation, and frame synchronization, a data frame structure based on dual spread spectrum code is designed. A long spread spectrum code is used as the training sequence, which can be used for data frame detection and synchronization, Doppler estimation, and channel estimation. A short spread spectrum code is used to modulate the effective information data. A delay cross-correlation algorithm is used for Doppler estimation, and a correlation algorithm is used for channel estimation. For underwater networking, each user is assigned a different pair of spread spectrum codes. Simulation results show that the system has a good anti-multipath, anti-interference, and anti-Doppler performance, the bit error rate can be smaller than 10^(-6) when the signal-to-noise ratio is larger than-10 dB, the data rate can be as high as 355 bits/s, and the system can be used in the downlink of CDMA based networks.
基金supported by the Key-Areas Research and Development Program of Guangdong Province(2020B020220004)the Youth Innovation Promotion Association,Chinese Academy of Sciences(2017399)+2 种基金the Science and Technology Program of Guangzhou(202002030097)the Hong Kong Research Grants Council Area of Excellence Scheme(AoE/M-403/16),the ECS(27204518)TRS of the HKSAR government(T21-705/20-N).
文摘The Human Genome Project opened an era of(epi)genomic research,and also provided a platform for the development of new sequencing technologies.During and after the project,several sequencing technologies continue to dominate nucleic acid sequencing markets.Currently,Illumina(short-read),PacBio(long-read),and Oxford Nanopore(longread)are the most popular sequencing technologies.Unlike PacBio or the popular short-read sequencers before it,which,as examples of the second or so-called Next-Generation Sequencing platforms,need to synthesize when sequencing,nanopore technology directly sequences native DNA and RNA molecules.Nanopore sequencing,therefore,avoids converting mRNA into cDNA molecules,which not only allows for the sequencing of extremely long native DNA and full-length RNA molecules but also document modifications that have been made to those native DNA or RNA bases.In this review on direct DNA sequencing and direct RNA sequencing using Oxford Nanopore technology,we focus on their development and application achievements,discussing their challenges and future perspective.We also address the problems researchers may encounter applying these approaches in their research topics,and how to resolve them.
基金This work was supported by the National Natural Science Foundation of China(Grant No.60472053)the Natural Science Foundation of Jiangsu Province(No.BK2003055)the Specialized Research Fund for the Doctoral Program of Higher Education(No.20030286017).
文摘Based on the brief account of the performance analysis result of the direct sequence spread spectrum(DSSS)system against a single tone continuous wave(CW)interference obtained from the traditional standard Gaussian approximation(SGA)hypothesis,the mathematical expression of the interference component of the symbol decision variable in the periodic sequence DSSS system under CW interference was deduced and the actual performance of the periodic sequence DSSS system against CW interference was researched through theoretical analysis and numerical simulations.The results indicate that the interference component of the symbol decision variable in the periodic sequence DSSS system under CW interference operates at a constant level or fluctuate monochromatically,which does not approach the standard Gaussian distribution,and the actual performance of the periodic sequence DSSS system against CW interference is completely different from the analytic result resorted to the standard Gaussian approximation(SGA).The bit error performance is correlative not only with the interference-signal ratio(ISR),the frequency offset and the phase of the CW interference sensitively,but also with the individual spread spectrum code sequence.
文摘Direction of arrival(DOA)estimation is one of the key technologies in smart antennas in the direct sequence ultra wideband(DS-UWB)system.Traditional DOA estimation methods based on narrow-band signals are not suitable for such system.Therefore,a fourth-order cumulant-based estimation method of DOA for DS-UWB signal is proposed.This method is set on the frequency domain model of DS-UWB array signal.Simulation results show that the algorithm is effective and can guarantee adequate estimation accuracy.
